A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report generated on 2020-02-03, 14:21 based on data in:
/hps/research1/birney/users/adrien/analyses/medaka_RNA_illumina/Indigene_pilot/RNA_pipeline2/results
General Statistics
Showing 580 samples.
featureCounts
Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Samtools
Samtools is a suite of programs for interacting with high-throughput sequencing data.
Percent Mapped
Alignment metrics from samtools stats; mapped vs. unmapped reads.
For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.
Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Alignment metrics
This module parses the output from samtools stats. All numbers in millions.
Samtools Flagstat
This module parses the output from samtools flagstat. All numbers in millions.
Mapped reads per contig
The samtools idxstats tool counts the number of mapped reads per chromosome / contig. Chromosomes with < 0.1% of the total aligned reads are omitted from this plot.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Salmon
Salmon is a tool for quantifying the expression of transcripts using RNA-seq data.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
STAR
STAR is an ultrafast universal RNA-seq aligner.
Alignment Scores
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
fastp
fastp An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...)
Filtered Reads
Filtering statistics of sampled reads.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Duplication Rates
Duplication rates of sampled reads.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Insert Sizes
Insert size estimation of sampled reads.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Sequence Quality
Average sequencing quality over each base of all reads.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
GC Content
Average GC content over each base of all reads.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
N content
Average N content over each base of all reads.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
